Strain identifier
BacDive ID: 133282
Type strain:
Species: Paracoccus contaminans
Strain Designation: WPAn02, RKI16-01929
Strain history: CIP <- 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain WPAn02
NCBI tax ID(s): 1945662 (species)
General
@ref: 25118
BacDive-ID: 133282
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, coccus-shaped
description: Paracoccus contaminans WPAn02 is an aerobe, Gram-negative, coccus-shaped bacterium that was isolated from contaminated axenic water microcosm.
NCBI tax id
- NCBI tax id: 1945662
- Matching level: species
strain history
@ref | history |
---|---|
42176 | 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain WPAn02 |
118738 | CIP <- 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain WPAn02 |
doi: 10.13145/bacdive133282.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Paracoccus
- species: Paracoccus contaminans
- full scientific name: Paracoccus contaminans Kämpfer et al. 2016
@ref: 25118
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Paracoccus
species: Paracoccus contaminans
strain designation: WPAn02, RKI16-01929
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
25118 | negative | 1 µm | 1 µm | coccus-shaped | no |
118738 | positive | coccus-shaped | yes |
colony morphology
- @ref: 25118
- colony size: 2 mm
- colony color: beige
- incubation period: 2 days
- medium used: NA (Nutrient Agar)
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
25118 | NA (Nutrient Agar) | yes | ||
25118 | brain–heart infusion agar | yes | ||
25118 | TSA (Trypticase soy agar) | yes | ||
25118 | Reasoner's 2A agar (R2A) | yes | ||
25118 | MacConkey agar | yes | ||
42176 | MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati | yes | Distilled water make up to (1000.000 ml);R2A agar (18.200 g) | |
118738 | CIP Medium 566 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
25118 | positive | growth | 10.0-45.0 | |
25118 | no | growth | 4 | psychrophilic |
25118 | no | growth | 45 | thermophilic |
42176 | positive | growth | 25 | mesophilic |
culture pH
- @ref: 25118
- ability: positive
- type: growth
- pH: 5.0-7.5
Physiology and metabolism
oxygen tolerance
- @ref: 25118
- oxygen tolerance: aerobe
spore formation
- @ref: 25118
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
25118 | NaCl | positive | growth | 0.0-1.0 %(w/v) |
25118 | NaCl | no | growth | 2 %(w/v) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
25118 | 30916 | 2-oxoglutarate | - | carbon source |
25118 | 16193 | 3-hydroxybenzoate | - | carbon source |
25118 | 16865 | gamma-aminobutyric acid | - | carbon source |
25118 | 17879 | 4-hydroxybenzoate | - | carbon source |
25118 | 17128 | adipate | - | carbon source |
25118 | 15963 | ribitol | - | carbon source |
25118 | 18305 | arbutin | - | carbon source |
25118 | 35391 | aspartate | - | carbon source |
25118 | 78208 | azelaate | - | carbon source |
25118 | 16383 | cis-aconitate | - | carbon source |
25118 | 16947 | citrate | - | carbon source |
25118 | 17057 | cellobiose | - | carbon source |
25118 | 16899 | D-mannitol | - | carbon source |
25118 | 28053 | melibiose | - | carbon source |
25118 | 16551 | D-trehalose | - | carbon source |
25118 | 65327 | D-xylose | - | carbon source |
25118 | 37054 | 3-hydroxybutyrate | - | carbon source |
25118 | 24265 | gluconate | - | carbon source |
25118 | 17859 | glutaric acid | - | carbon source |
25118 | 17268 | myo-inositol | - | carbon source |
25118 | 17240 | itaconate | - | carbon source |
25118 | 15603 | L-leucine | - | carbon source |
25118 | 15729 | L-ornithine | - | carbon source |
25118 | 17295 | L-phenylalanine | - | carbon source |
25118 | 62345 | L-rhamnose | - | carbon source |
25118 | 16828 | L-tryptophan | - | carbon source |
25118 | 68428 | maltitol | - | carbon source |
25118 | 36986 | mesaconate | - | carbon source |
25118 | 28037 | N-acetylgalactosamine | - | carbon source |
25118 | 506227 | N-acetylglucosamine | - | carbon source |
25118 | 18401 | phenylacetate | - | carbon source |
25118 | 17272 | propionate | - | carbon source |
25118 | 17148 | putrescine | - | carbon source |
25118 | 17814 | salicin | - | carbon source |
25118 | 9300 | suberic acid | - | carbon source |
25118 | 17992 | sucrose | - | carbon source |
25118 | 15708 | trans-aconitate | - | carbon source |
25118 | 30089 | acetate | + | carbon source |
25118 | 15824 | D-fructose | + | carbon source |
25118 | 12936 | D-galactose | + | carbon source |
25118 | 17634 | D-glucose | + | carbon source |
25118 | 17306 | maltose | + | carbon source |
25118 | 16024 | D-mannose | + | carbon source |
25118 | 16988 | D-ribose | + | carbon source |
25118 | 17924 | D-sorbitol | + | carbon source |
25118 | 29806 | fumarate | + | carbon source |
25118 | 16977 | L-alanine | + | carbon source |
25118 | 30849 | L-arabinose | + | carbon source |
25118 | 15971 | L-histidine | + | carbon source |
25118 | 17115 | L-serine | + | carbon source |
25118 | 24996 | lactate | + | carbon source |
25118 | 15361 | pyruvate | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
25118 | catalase | + | 1.11.1.6 |
25118 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | enrichment culture | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
25118 | contaminated axenic water microcosm | R2A agar (Reasoner's 2A agar) | ||||
118738 | Other, Contaminant of an axenic E. coli culture in 7% NaCl | Weningerode | Germany | DEU | Europe |
isolation source categories
Cat1 | Cat2 |
---|---|
#Engineered | #Contamination |
#Environmental | #Aquatic |
#Host | #Microbial |
taxonmaps
- @ref: 69479
- File name: preview.99_5288.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1674;97_3137;98_3939;99_5288&stattab=map
- Last taxonomy: Paracoccus contaminans subclade
- 16S sequence: KX427102
- Sequence Identity:
- Total samples: 755
- soil counts: 31
- aquatic counts: 127
- animal counts: 590
- plant counts: 7
Safety information
risk assessment
- @ref: 118738
- biosafety level: 1
- biosafety level comment: Risk group (French classification)
Sequence information
16S sequences
- @ref: 25118
- description: Paracoccus contaminans strain WPAn02 16S ribosomal RNA gene, partial sequence
- accession: KX427102
- length: 1397
- database: nuccore
- NCBI tax ID: 1945662
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paracoccus contaminans strain RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T | 1945662.5 | plasmid | patric | 1945662 |
66792 | Paracoccus contaminans strain RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T | 1945662.3 | complete | patric | 1945662 |
GC content
- @ref: 25118
- GC-content: 66.1
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 73.176 | yes |
gram-positive | no | 97.544 | yes |
anaerobic | no | 99.075 | yes |
aerobic | yes | 92.167 | no |
halophile | no | 83.842 | yes |
spore-forming | no | 96.56 | no |
glucose-util | yes | 84.383 | yes |
flagellated | no | 93.949 | no |
thermophile | no | 74.787 | no |
glucose-ferment | no | 92.201 | no |
External links
@ref: 25118
culture collection no.: RKI 16-01929, LMG 29738, CCM 8701, CIP 111112
straininfo link
- @ref: 91401
- straininfo: 412579
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 27599853 | Paracoccus contaminans sp. nov., isolated from a contaminated water microcosm. | Kampfer P, Aurass P, Karste S, Flieger A, Glaeser SP | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001478 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Microbiology | Transcriptome |
Genetics | 28596405 | Genome Sequence of Paracoccus contaminans LMG 29738(T), Isolated from a Water Microcosm. | Aurass P, Karste S, Trost E, Glaeser SP, Kampfer P, Flieger A | Genome Announc | 10.1128/genomeA.00487-17 | 2017 | Phylogeny | |
Phylogeny | 31913112 | Paracoccus aeridis sp. nov., an indole-producing bacterium isolated from the rhizosphere of an orchid, Aerides maculosa. | Rai A, N S, G S, A S, G D, Ch S, Ch V R | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003962 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, India, Indoleacetic Acids/chemistry, Nucleic Acid Hybridization, Orchidaceae/*microbiology, Paracoccus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | journal | pubmed | catalogue |
---|---|---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
25118 | P. A. Kämpfer, P.,Karste, S.,Flieger, A.,Glaeser, S. P. | Paracoccus contaminans sp. nov., isolated from a contaminated water microcosm | 10.1099/ijsem.0.001478 | IJSEM 66: 5101-5105 2016 | 27599853 | |
42176 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/34937 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
91401 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID412579.1 | |||
118738 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111112 | Collection of Institut Pasteur (CIP 111112) |